[MOBY-dev] Re: [moby] buggy new biomoby release

[Rebecca Ernst]

Hi Mark!

We tried once more and installed the new release (0.8.2).

The problems we can see are that our perl services are not working 
anymore ("service returned no response") the bad thing is that it 
doesn't give any error so we have no clue where the problem is.
Gbrowse works - the services can be listed and non-MIPS services and 
MIPS Java services can be executed. So Moby Central obviously works okay 
since (since we added the column lsid to the db)

We then tried to remove the method "_getServiceInstanceRDF" in the 
MOBY/Central.pm because in there it uses lsid but this didn't solve 
anything.

Just in case we find the problem and you build a new release I have some 
more suggestions leading to even more user-friendlyness ;-) :

- include all libraries not only the perl libraries because all former 
releases contained everything and now we have to get the other libs from 
older releases and that means copying it. I guess that most people would 
expect that they get a full release otherwise consider renaming it (not 
biomoby release but perl_lib_release)

- don't rename the moby-live path to moby-live_API_releasewhatever it 
now requires that people move it (or adjust their pathes)

- next to the link (for downloading the release) add the information 
that for database provider they will have to change their database
("alter table service_instance add lsid VARCHAR (255) NOT NULL default 
''; ")

Cheers!
Rebecca




Mark Wilkinson wrote:

>Doh!  I missed one.  
>
>There is an (unused) call to LS::ID->new in the code. Unfortunately, I
>do have the LSID libraries installed so I didn't pick up on that.
>
>I have commented-out the line in the release codebase and will make
>another release, but before I do I want to make sure that this was the
>only problem you saw.
>
>Let me know,
>
>M
>
>
>
>
>On Mon, 2005-07-18 at 17:14 +0200, Rebecca Ernst wrote:
>  
>
>>Hi Mark (and rest)!
>>
>>As suggested Dirk and I sat down today to do a cvs update to get the 
>>last stable release.
>>
>>Now it's 5 hours later and we gave up and switched back to the last 
>>working code we had (and which we luckily saved before doing the update! 
>>:-))
>>
>>There are several problems keeping us from updating our code:
>>
>>First of all the links on the release site (biomoby.org/releases) are 
>>crappy. The link to biomoby.0.8.2 links to biomoby.0.8.1 we didn't 
>>notice this and therefore received the older version. This version is 
>>VERY outdated and not functional (e.g.it uses DOM instead of LibXML)
>>
>>Then we modified the link to get 0.8.2. This version is also not 
>>functional as it uses lsid (although this was meant to be the version 
>>BEFORE the lsid change). Even when we added a column lsid to the 
>>database it didn't work (I guess one would also need the lsid resolver 
>>and so on.)
>>
>>Another try was to do an cvs update which crashed everything as 
>>completely buggy and syntactical wrong code was checked in (especially 
>>in Adaptor/.../mysql.pm)
>>
>>
>>So luckily we could rescue everything because of our save but I guess 
>>this is not the way to make people happy installing BioMoby :-(
>>
>>Could we please make sure that releases are functional and the code in 
>>the cvs is not complete crap.... otherwise I'll have to do some more 
>>spanking ;-)
>>
>>
>>Cheers,
>>Rebecca
>>
>>
>>
>>
>>
>>
>>    
>>

-- 
Rebecca Ernst
MIPS, Inst. for Bioinformatics
GSF Research Center for Environment and Health
Ingolstaedter Landstr. 1
85764 Neuherberg
fon: +49 89 3187 3583
email: Rebecca.Ernst at gsf.de